Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_013451009.1 CALNI_RS04425 1-pyrroline-5-carboxylate dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_000183405.1:WP_013451009.1 Length = 546 Score = 184 bits (467), Expect = 7e-51 Identities = 137/457 (29%), Positives = 230/457 (50%), Gaps = 22/457 (4%) Query: 15 SGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGEL 74 +G++ + P + HVLA+ + +V AI ++ + EW + +R SI LKA +L Sbjct: 56 TGDKGKIVCPHNHGHVLAEYHKAGEKEVLLAIEESQKAWKEWQKLRYEERISIFLKAADL 115 Query: 75 MEQEAQEF---ALLMTLEEG--KTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPN 129 + + + A ++++ + + DS E+ + +Y +K P N Sbjct: 116 LSTKYRYLLNAATMLSISKNAYQAEIDSACELIDFWRFNSYYAQQIYKEQPLYSPKGTWN 175 Query: 130 TRIFTVKEPL-GVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVL 188 +T + PL G + +TP+NF +PA+ GN + KPA+ ++++L Sbjct: 176 ---YTQQRPLEGFIFAVTPFNFTAIGGNLPTSPAIM-GNVVLWKPASSAIYAPYFIMKIL 231 Query: 189 SKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVG----NKNRMT 244 +AGLP+GV+N + G S VGD + +A + FTGST V ++++K VG Sbjct: 232 QEAGLPDGVINFIPGSASIVGDICIKHPLMAGIHFTGSTAVFQKMWKDVGANIAKYTNYP 291 Query: 245 RIQLELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLL 304 RI E GGK+ ++ SAD+ VRG F GQ C+A SR I + ++ + + + Sbjct: 292 RIVGETGGKDFVFAHSSADIKKLVVALVRGAFEYQGQKCSAASRAYIPRSIWGKTWEIME 351 Query: 305 ERVKKWRVGPGTEDVDM-GPVVDEGQFKKDLEYIEYGKN-VGAKLIYGGNIIPGKGYFLE 362 +K ++G + ++ V+DE F+ EYI+Y KN A++I+GG GYF+E Sbjct: 352 AELKNLKMGDVEDFTNLINAVIDESAFESITEYIDYAKNSKDAEIIFGGKYDKSIGYFIE 411 Query: 363 PTIFEGVTSDMRLFKEEIFGPVLS--VTEAKDLDEAIRLVNAVD-YGHTAGIVASDIKAI 419 PT+ + +EEIFGPVL+ V + + +E + + + Y T I A+D K I Sbjct: 412 PTVILAKDPHFKTMEEEIFGPVLTIYVYDDEKFEETLEICDRTSPYALTGAIFANDRKVI 471 Query: 420 NEFVSRVE--AGVIKVN-KPTVGLELQAPFGGFKNSG 453 + + ++E AG +N KPT + Q PFGG + SG Sbjct: 472 SMMMEKLEFAAGNFYINDKPTGAVVGQQPFGGGRASG 508 Lambda K H 0.316 0.135 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 682 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 478 Length of database: 546 Length adjustment: 35 Effective length of query: 443 Effective length of database: 511 Effective search space: 226373 Effective search space used: 226373 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory